This document provides an overview of the Unispec Data collected by terrestrial RA Ruby An in 2017, 2018, 2019, and 2020.
Unispec Data was collected approximately weekly. Unispec locations were changed by Jim and Ruby from historic locations to standardized spots, mainly outside of the destructive zones. See —- file for map comparison.
INSTRUMENT PROTOCOL LOCATIONS DATA
On – the XXX foreoptic broke at the Shrub plots. Look for inconsistenies here with the rest of the season.
Unispec data was collected when weather permitted, weekly if possible. The summer was exceptionally rainy and vegetation was often wet, restricting the possible sampling times. At the end of the season, silver circular tags were nailed to the boardwalk at each unispec location (where line-segment perpendicular to the edge of the plot hit the boardwalk). This location was determined by measuring with a string and measuring tape along the plot edge between the wooden stakes marking each 5m segment of the plot.
Drone data was collected in 2018 in conjunction with unispec measurements; however, this data
turned out to be unusable due to a calibration error of the drone sensor.
Unispec data was collected approximately weekly. The MAT06 & MAT89 sites given highest priority, the historic and wet sedge least so. The SHB89 sites were only unispec’d once. On —- 15 scans were made per plot for comparison purposes. On —- the default number of scans per plot was increased from 5 to 10 for all sites. It took a couple tries to land on “the most efficient” 10 spots to take the scans, so there is some variability over the course of the summer on where these “additional” measurements were made in each plot.
The data collected in 2019 is saved in the following 4 files.
Metadata correspondence key of scan (.spu file) to sample location.
Summary file for analysis
## This chunk of code tallies the number of files in the raw, processed, and index data dataframes and displays the output in a table.
## Raw Data summary
spu_dataframe <- full_join(spu_spectra, spu_key) %>%
mutate(DateTime = with_tz(DateTime, "US/Alaska")) %>%
# Add Date & ARC-LTER Site
mutate(Date = lubridate::date(DateTime)) %>%
mutate(Site = str_extract(spu_filename, "([A-Z]{3,8}[0-9]*)(?=_)")) %>% # DOES NOT WORK FOR "MAT-SH" measurements
mutate(Site = ifelse(str_detect(spu_filename, "MAT-SH"), "MAT-SH", Site))
## Joining, by = c("spu_filename", "DateTime")
raw_files <- spu_dataframe %>% group_by(Date, Site) %>%
summarize(Raw_Files = n_distinct(spu_filename))
## `summarise()` has grouped output by 'Date'. You can override using the `.groups` argument.
## Processed Data summary
processed_files <- left_join(processed_spectra, spu_key) %>%
# Add Date & ARC-LTER Site
mutate(DateTime = with_tz(DateTime, "US/Alaska")) %>%
mutate(Date = lubridate::date(DateTime)) %>%
mutate(Site = str_extract(spu_filename, "([A-Z]{3,8}[0-9]*)(?=_)")) %>% # DOES NOT WORK FOR "MAT-SH" measurements
mutate(Site = ifelse(str_detect(spu_filename, "MAT-SH"), "MAT-SH", Site)) %>%
## Summarize
group_by(Date, Site) %>%
summarize(Processed_Files = n_distinct(spu_filename))
## Joining, by = c("spu_filename", "DateTime")
## `summarise()` has grouped output by 'Date'. You can override using the `.groups` argument.
## Index Data summary
index_files <- left_join(index_data, spu_key) %>%
# Add Date & ARC-LTER Site
mutate(DateTime = with_tz(DateTime, "US/Alaska")) %>%
mutate(Date = lubridate::date(DateTime)) %>%
mutate(Site = str_extract(spu_filename, "([A-Z]{3,8}[0-9]*)(?=_)")) %>% # DOES NOT WORK FOR "MAT-SH" measurements
mutate(Site = ifelse(str_detect(spu_filename, "MAT-SH"), "MAT-SH", Site)) %>%
## Summarize
group_by(Date, Site) %>%
summarize(Index_Files = n_distinct(spu_filename))
## Joining, by = c("spu_filename", "DateTime")
## `summarise()` has grouped output by 'Date'. You can override using the `.groups` argument.
## DISPLAY
kable(full_join(raw_files, processed_files) %>% full_join(index_files) %>% arrange(Date, Site))
## Joining, by = c("Date", "Site")
## Joining, by = c("Date", "Site")
| Date | Site | Raw_Files | Processed_Files | Index_Files |
|---|---|---|---|---|
| 2019-06-02 | LMAT | 246 | 244 | 239 |
| 2019-06-02 | MAT | 122 | 121 | 116 |
| 2019-06-02 | TEST | 22 | 20 | 15 |
| 2019-06-08 | DHT | 171 | 170 | 165 |
| 2019-06-08 | LMAT | 50 | 50 | 50 |
| 2019-06-08 | WSG1 | 31 | 30 | 25 |
| 2019-06-11 | EDC | 16 | NA | NA |
| 2019-06-11 | LMAT | 186 | 185 | 180 |
| 2019-06-11 | MAT | 100 | 100 | 100 |
| 2019-06-11 | SHB2 | 26 | 25 | 20 |
| 2019-06-11 | WSG23 | 46 | 45 | 40 |
| 2019-06-15 | DHT | 171 | 170 | 165 |
| 2019-06-15 | HIST | 46 | 45 | 40 |
| 2019-06-15 | MNAT | 90 | 90 | 90 |
| 2019-06-15 | NANT | 66 | 65 | 60 |
| 2019-06-18 | LMAT | 558 | 556 | 546 |
| 2019-06-18 | MAT | 307 | 307 | 300 |
| 2019-06-18 | WSG1 | 60 | 60 | 50 |
| 2019-06-19 | WSG23 | 101 | 90 | 80 |
| 2019-06-20 | MNAT | 255 | 255 | 240 |
| 2019-06-20 | NANT | 191 | 190 | 180 |
| 2019-06-21 | DHT | 244 | 242 | 232 |
| 2019-06-22 | DHT | 146 | 119 | 109 |
| 2019-06-22 | HIST | 203 | 195 | 175 |
| 2019-06-24 | LMAT | 40 | NA | NA |
| 2019-06-26 | COMP | 113 | 112 | 107 |
| 2019-06-26 | LMAT | 186 | 186 | 181 |
| 2019-06-26 | MAT | 226 | 225 | 220 |
| 2019-06-27 | LMAT | 159 | 155 | 150 |
| 2019-06-27 | MNAT | 131 | 130 | 120 |
| 2019-07-02 | DHT | 171 | 170 | 165 |
| 2019-07-02 | HIST | 131 | 125 | 120 |
| 2019-07-02 | LMAT | 306 | 305 | 290 |
| 2019-07-02 | LMATEDC | 9 | NA | NA |
| 2019-07-02 | MAT | 231 | 226 | 220 |
| 2019-07-02 | MAT-SH | 38 | 37 | 32 |
| 2019-07-04 | MNAT | 131 | 130 | 120 |
| 2019-07-04 | NANT | 140 | 140 | 130 |
| 2019-07-06 | LMAT | 76 | 75 | 70 |
| 2019-07-06 | LMATEDC | 3 | NA | NA |
| 2019-07-06 | WSG1 | 56 | 55 | 45 |
| 2019-07-08 | MAT | 22 | 20 | 15 |
| 2019-07-09 | LMAT | 286 | 285 | 280 |
| 2019-07-09 | LMATEDC | 6 | NA | NA |
| 2019-07-09 | MAT | 227 | 225 | 220 |
| 2019-07-12 | DHT | 191 | 190 | 180 |
| 2019-07-12 | HIST | 131 | 130 | 120 |
| 2019-07-12 | LMAT | 91 | 90 | 70 |
| 2019-07-12 | MNAT | 131 | 130 | 120 |
| 2019-07-15 | DHT | 26 | 25 | 20 |
| 2019-07-15 | LMAT | 51 | 50 | 40 |
| 2019-07-15 | TEST | 94 | 80 | 80 |
| 2019-07-18 | LMAT | 292 | 290 | 280 |
| 2019-07-18 | MAT | 226 | 225 | 220 |
| 2019-07-22 | MNAT | 51 | 50 | 40 |
| 2019-07-22 | NANT | 45 | 45 | 40 |
| 2019-07-23 | DHT | 201 | 200 | 195 |
| 2019-07-23 | HIST | 131 | 130 | 120 |
| 2019-07-23 | WSG23 | 86 | 85 | 80 |
| 2019-07-24 | MAT | 226 | 225 | 220 |
| 2019-07-25 | EDC | 6 | NA | NA |
| 2019-07-25 | LMAT | 291 | 290 | 280 |
| 2019-07-30 | MNAT | 141 | 140 | 120 |
| 2019-07-30 | NANT | 135 | 135 | 120 |
| 2019-07-31 | DHT | 77 | 75 | 65 |
| 2019-07-31 | HIST | 46 | 45 | 40 |
| 2019-07-31 | LMAT | 81 | 80 | 70 |
| 2019-07-31 | MAT | 62 | 60 | 55 |
| 2019-07-31 | WSG1 | 61 | 60 | 50 |
| 2019-08-02 | LMAT | 291 | 290 | 280 |
| 2019-08-02 | LMATEDC | 6 | NA | NA |
| 2019-08-02 | MAT | 226 | 225 | 220 |
| 2019-08-05 | DHT | 206 | 205 | 195 |
| 2019-08-07 | LMAT | 290 | 290 | 280 |
| 2019-08-07 | MAT | 226 | 225 | 220 |
| 2019-08-07 | MNAT | 131 | 130 | 120 |
| 2019-08-10 | HIST | 131 | 130 | 120 |
| 2019-08-16 | DHT | 226 | 225 | 215 |
| 2019-08-16 | LMAT | 347 | 346 | 320 |
| 2019-08-16 | LMATEDC | 6 | 6 | 6 |
| 2019-08-16 | MAT | 344 | 342 | 317 |
| 2019-08-16 | MNAT | 172 | 171 | 161 |
| 2019-08-16 | NANT | 131 | 131 | 120 |
Code chunks:
## Joining, by = c("spu_filename", "DateTime")
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
Unispec data collected once at the following sites:
Unispec performed fine. The downward facing foreoptic seemed to be breaking a bit at the joint to the metal. However, checking the Darkscans it didn’t seem like any light was leaking in.